Abstract Background Bees are important environmental indicators, revealing pollution through mortality or residues in honey and other hive products. We compared honey quality in a rural (Western Milan) and an industrial area (Northern Milan-Rho) in Lombardy (Italy). Methods In collaboration with the local Health and Environmental Protection Agencies, we collect and evaluate data regarding organic and inorganic residues in the honey samples from 2011 to 2022. Furthermore, we investigate the possible sources of air emissions through INEMAR database (INventario EMissioni ARia). Results Tetracyclines were detected in one case in the rural area, while Pb concentration was found above legal limits in several samples in the industrial area. INEMAR evidenced combustion in industry and road transport as the main sources of Pb emission in that area. It was also noticed Hg emissions in the rural area, clearly higher than in other territories. Conclusions The fraudulent use of antibiotics to eliminate pathogens, such as Paenibacillus larvae, responsible for American foulbrood, can be at the origin of their presence in the honey. Continuous monitoring of these compounds is critical since their environmental persistence can be very long lasting and a risk for human health. Heavy metals are harmful for human health and can have natural and mostly anthropic origins. The main sources are motor traffic, exhaust gases and fumes, as well as pesticides and synthetic fertilizers. Pb contamination can derive from the location of the apiaries near roads with high vehicular traffic, but in some cases, from the paints used to waterproof hives. The unexpected high Hg emissions better address next monitoring on honey in the rural area where no in-depth Hg analysis has been carried out until now. This interdisciplinarity is a new approach and an essential tool to better understand the influence of anthropic activities and of air pollution on honey quality. Key messages • Comparison of chemical quality (organic and inorganic residues) in honey produced in rural and industrial areas in Lombardy (Northern Italy). • An interdisciplinary approach in honey quality assessment, considering estimated emission loads from anthropic activities in both areas.